Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userSimulation Modeling
92
0
0.0
(
0
)
Authors
Florian Hartig
Ask ChatGPT about the research
No Arabic abstract
With the rise of computers, simulation models have emerged beside the more traditional statistical and mathematical models as a third pillar for ecological analysis. Broadly speaking, a simulation model is an algorithm, typically implemented as a computer program, which propagates the states of a system forward. Unlike in a mathematical model, however, this propagation does not employ the methods of calculus but rather a set of rules or formulae that directly prescribe the next state. Such an algorithmic model specification is particularly suited for describing systems that are difficult to capture or analyze with differential equations such as: (a) systems that are highly nonlinear or chaotic; (b) discrete systems, for example networks or groups of distinct individuals; (c) systems that are stochastic; and (d) systems that are too complex to be successfully treated with classical calculus. As these situations are frequently encountered in ecology, simulation models are now widely applied across the discipline. They have been instrumental in developing new insights into classical questions of species coexistence, community assembly, population dynamics, biogeography, and many more. The methods for this relatively young field are still being actively developed, and practical work with simulation models requires ecologists to learn new skills such as coding, sensitivity analysis, calibration, validation, and forecasting uncertainties. Moreover, scientific inquiry with complex systems has led to subtle changes to the philosophical and epistemological views regarding simplicity, reductionism, and the relationship between prediction and understanding.
rate research
Read More
We present a computational model to reconstruct trees of ancestors for animals with sexual reproduction. Through a recursive algorithm combined with a random number generator, it is possible to reproduce the number of ancestors for each generation and use it to constraint the maximum number of the following generation. This new model allows to consider the reproductive preferences of particular species and combine several trees to simulate the behavior of a population. It is also possible to obtain a description analytically, considering the simulation as a theoretical stochastic process. Such process can be generalized in order to use an algorithm associated with it to simulate other similar processes of stochastic nature. The simulation is based in the theoretical model previously presented before.
The unwelcome evolution of malignancy during cancer progression emerges through a selection process in a complex heterogeneous population structure. In the present work, we investigate evolutionary dynamics in a phenotypically heterogeneous population of stem cells (SCs) and their associated progenitors. The fate of a malignant mutation is determined not only by overall stem cell and differentiated cell growth rates but also differentiation and dedifferentiation rates. We investigate the effect of such a complex population structure on the evolution of malignant mutations. We derive exact analytic results for the fixation probability of a mutant arising in each of the subpopulations. The analytic results are in almost perfect agreement with the numerical simulations. Moreover, a condition for evolutionary advantage of a mutant cell versus the wild type population is given in the present study. We also show that microenvironment-induced plasticity in invading mutants leads to more aggressive mutants with higher fixation probability. Our model predicts that decreasing polarity between stem and differentiated cells turnover would raise the survivability of non-plastic mutants; while it would suppress the development of malignancy for plastic mutants. We discuss our model in the context of colorectal/intestinal cancer (at the epithelium). This novel mathematical framework can be applied more generally to a variety of problems concerning selection in heterogeneous populations, in other contexts such as population genetics, and ecology.
We develop a modeling framework for bioluminescence light found in the deep sea near neutrino telescopes by combining a hydrodynamic model with a stochastic one. The bioluminescence is caused by organisms when exposed to a non-constant water flow, such as past the neutrino telescopes. We model the flow using the incompressible Navier-Stokes equations for Reynolds numbers between 4000 and 23000. The discretization relies on a finite element method which includes upwind-stabilization for the velocity field. On top of the flow model, we simulate a population of random microscopic organisms. Their movement and emission are stochastic processes which we model using Monte Carlo methods. We observe unique time-series for the photon counts depending on the flow velocity and detector specifications. This opens up the possibility of categorizing organisms using neutrino detectors. We show that the average light-yield and pulse shapes require precise flow modeling, while the emission timing is chaotic. From this we construct a fast modeling scheme, requiring only a subset of computationally expensive flow and population modeling.
Personalized models of the gut microbiome are valuable for disease prevention and treatment. For this, one requires a mathematical model that predicts microbial community composition and the emergent behavior of microbial communities. We seek a modeling strategy that can capture emergent behavior when built from sets of universal individual interactions. Our investigation reveals that species-metabolite interaction modeling is better able to capture emergent behavior in community composition dynamics than direct species-species modeling. Using publicly available data, we examine the ability of species-species models and species-metabolite models to predict trio growth experiments from the outcomes of pair growth experiments. We compare quadratic species-species interaction models and quadratic species-metabolite interaction models, and conclude that only species-metabolite models have the necessary complexity to to explain a wide variety of interdependent growth outcomes. We also show that general species-species interaction models cannot match patterns observed in community growth dynamics, whereas species-metabolite models can. We conclude that species-metabolite modeling will be important in the development of accurate, clinically useful models of microbial communities.
In this paper, a model for understanding the effects of selection using systems- level computational approaches is introduced. A number of concepts and principles essential for understanding the motivation for constructing the model will be introduced first. This will be followed by a description of parameters, measurements, and graphical representations used in the model. Four possible outcomes for this model are then introduced and described. In addition, the relationship of relative fitness to selection is described. Finally, the consequences and potential lessons learned from the model are discussed.
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
